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- PDB-7k0w: The crystal structure of the 2009/H1N1/California PA endonuclease... -

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Basic information

Entry
Database: PDB / ID: 7k0w
TitleThe crystal structure of the 2009/H1N1/California PA endonuclease (construct with truncated loop 51-72) in complex with Baloxavir acid
ComponentsPolymerase acidic protein
KeywordsVIRAL PROTEIN / HYDROLASE / virus / nuclease / cap-snatching
Function / homology
Function and homology information


cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / viral RNA genome replication / DNA-templated transcription / host cell nucleus ...cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / viral RNA genome replication / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding
Similarity search - Function
Polymerase acidic protein / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA
Similarity search - Domain/homology
Baloxavir acid / : / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsKumar, G. / White, S.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI098757 United States
CitationJournal: To Be Published
Title: Crystal structure of the influenza virus PA endonuclease in complex with Baloxavir Acid
Authors: Kumar, G. / White, S.W.
History
DepositionSep 6, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9346
Polymers23,1481
Non-polymers7855
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Protein elutes as a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.718, 89.718, 133.763
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Polymerase acidic protein / RNA-directed RNA polymerase subunit P2


Mass: 23148.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Loop 51-72 is replaced with a GGS linker
Source: (gene. exp.) Influenza A virus (strain swl A/California/04/2009 H1N1)
Strain: swl A/California/04/2009 H1N1 / Gene: PA / Plasmid: pET52b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: C3W5S0, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-E4Z / Baloxavir acid


Mass: 483.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H19F2N3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.1M HEPES pH 7.8, 1.0M Ammonium Sulfate, 10mM MnCl2, 10mM MgCl2, 0.5% PVP K15

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 15263 / % possible obs: 92.5 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.031 / Rrim(I) all: 0.096 / Χ2: 0.903 / Net I/σ(I): 8.6 / Num. measured all: 132352
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.09-2.164.60.5629200.8350.2510.6190.6557.7
2.16-2.255.50.56612320.8710.2340.6160.67175.5
2.25-2.356.80.59314710.8650.2290.6380.70191.1
2.35-2.488.70.49816090.9460.1760.530.70398.9
2.48-2.639.80.38816400.9680.1290.4090.7699.9
2.63-2.84100.28516250.980.0940.3010.83699.9
2.84-3.129.90.15816330.9930.0530.1670.93299.9
3.12-3.579.90.08516690.9970.0280.091.033100
3.57-4.59.70.05916770.9980.020.0621.077100
4.5-508.90.05517870.9980.020.0591.21999.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DES

5des


Resolution: 2.09→44.86 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2485 806 5.28 %
Rwork0.2163 14449 -
obs0.218 15255 92.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.16 Å2 / Biso mean: 50.5359 Å2 / Biso min: 26.6 Å2
Refinement stepCycle: final / Resolution: 2.09→44.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1462 0 46 22 1530
Biso mean--51.37 45.04 -
Num. residues----179
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.09-2.220.378890.29761620170964
2.22-2.390.36181240.28622315243990
2.4-2.640.34631260.275325972723100
2.64-3.020.34061480.259625652713100
3.02-3.80.2311460.2126132759100
3.8-44.860.1981730.180627392912100

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